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http://www.bioconductor.org/packages/release/bioc/html/TEQC.html

An R/Bioconductor package for quality assessment of target enrichment experiments. This package provides functionalities for assessing and visualizing the quality of the target enrichment process, like specificity and sensitivity of the capture, per-target read coverage and so on.

Proper citation: TEQC (RRID:SCR_001943) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/flowViz.html

Software that provides visualization tools for flow cytometry data.

Proper citation: flowViz (RRID:SCR_002075) Copy   

•   Source: SciCrunch Registry

https://www.bioconductor.org/packages//2.11/bioc/html/flowQB.html

A fully automated R Bioconductor package to calculate automatically the detector efficiency (Q), optical background (B) and intrinsic CV of the beads.

Proper citation: flowQB (RRID:SCR_002144) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/flowFit.html

A Bioconductor package designed to perform quantitative analysis of cell proliferation in tracking dye-based experiments. The package uses an R implementation of the Levenberg-Marquardt algorithm (minpack.lm) to fit a set of peaks (corresponding to different generations of cells) over the proliferation-tracking dye distribution in a FACS experiment.

Proper citation: flowFit (RRID:SCR_002286) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/2.13/bioc/html/spliceR.html

An easy-to-use R package for classification of alternative splicing and prediction of coding potential from RNA-seq data.

Proper citation: spliceR (RRID:SCR_002280) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/flowPlots.html

Software for analysis plots and data class for gated flow cytometry data.

Proper citation: flowPlots (RRID:SCR_002177) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/flowCore.html

A Bioconductor software package for high throughput flow cytometry that provides S4 data structures and basic functions.

Proper citation: flowCore (RRID:SCR_002205) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/flowBeads.html

Software package for the analysis of flow cytometry bead data. It extends flowCore to provide functionality specific to bead data. One of the goals of this package is to automate analysis of bead data for the purpose of normalization.

Proper citation: flowBeads (RRID:SCR_002440) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/flowCyBar.html

A software package to analyze flow cytometric data using gate information to follow population / community dynamics.

Proper citation: flowCyBar (RRID:SCR_002319) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/devel/bioc/html/MBASED.html

Software package containing functions for allele-specific gene expression (ASE) analysis using meta-analysis based allele-specific expression detection.

Proper citation: MBASED (RRID:SCR_002584) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/2.12/bioc/html/DNAcopy.html

Software that segments DNA copy number data using circular binary segmentation to detect regions with abnormal copy number.

Proper citation: DNAcopy (RRID:SCR_012560) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/ExiMiR.html

R functions for the normalization of Exiqon miRNA array data.

Proper citation: ExiMiR (RRID:SCR_012753) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/motifRG.html

Software tools for discriminative motif discovery using regression methods.

Proper citation: motifRG (RRID:SCR_012602) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/MiRaGE.html

Software package that contains functions for inference of target gene regulation by miRNA, based on only target gene expression profile.

Proper citation: MiRaGE (RRID:SCR_012738) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/CexoR.html

Software for strand specific peak-pair calling in ChIP-exo replicates.

Proper citation: CexoR (RRID:SCR_012769) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/tRanslatome.html

Detection of differentially expressed genes (DEGs) from the comparison of two biological conditions among different levels of gene expression, using several statistical methods: Rank Product, t-test, SAM, Limma, ANOTA, DESeq, edgeR.

Proper citation: tRanslatome (RRID:SCR_012810) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/BicARE.html

Biclustering Analysis and Results Exploration.

Proper citation: BicARE (RRID:SCR_012881) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/charm.html

Function for differentially methylated regions (DMR) detection that is a part of the charm package in R/Bioconductor.

Proper citation: dmrFinder (RRID:SCR_012853) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/ChIPpeakAnno.html

Software package that includes functions to retrieve the sequences around the peak, obtain enriched Gene Ontology terms, find the nearest gene, exon, miRNA or custom features such as most conserved elements.

Proper citation: ChIPpeakAnno (RRID:SCR_012828) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/inSilicoMerging.html

Collection of techniques to remove inter-study bias when combining gene expression data originating from different studies.

Proper citation: inSilicoMerging (RRID:SCR_012829) Copy   

•   Source: SciCrunch Registry